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CRISPR and crRNAs

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...

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Updated: Dec 19, 2025

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Published on: September 4, 2019

Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen.

Qingkai Song^1,2, Ke Ni^1,2, Min Liu^1,2

¹School of Life Sciences, Westlake University, Hangzhou, 310024, China.

|June 10, 2020

Summary

This summary is machine-generated.

This study introduces Direct-seq, a novel CRISPR screening method. It efficiently profiles CRISPR perturbations and transcriptional readouts together in single cells using scRNA-seq.

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Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

CRISPR-based genome perturbation is powerful for genetic screens.
Assaying complex molecular readouts at scale after perturbation remains challenging.

Purpose of the Study:

To develop a high-resolution, scalable method for profiling CRISPR perturbations and their transcriptional consequences.
To streamline the workflow for analyzing CRISPR-mediated genetic screens.

Main Methods:

Engineered guide RNA (gRNA) scaffolds with a mixed A/G capture sequence.
Direct reverse transcription of gRNA transcripts alongside endogenous mRNA using poly (dT) primers.
High-content molecular phenotyping via single-cell RNA sequencing (scRNA-seq).

Main Results:

Demonstrated simultaneous profiling of CRISPR perturbations and transcriptional readouts.
Enabled direct reverse transcription of gRNA transcripts.
Facilitated high-content molecular phenotyping within a streamlined workflow.

Conclusions:

Direct-seq offers a streamlined approach for CRISPR screening.
The method allows for simultaneous analysis of perturbations and transcriptional responses.
This advances high-resolution, large-scale molecular phenotyping in genetic screens.